<?xml version="1.0"?>
<tool id="PSM.Prep" name="PSM Prep" version="1.94.2">
  <description>prepares data for the PSM Plotter</description>
  <version_command>perl cpt_psm_0_prep.pl --version</version_command>
  <stdio>
    <exit_code range="1:" level="fatal"/>
  </stdio>  
  <requirements>
      <requirement type="package" version="5.22.1">perl</requirement>
      <requirement type="package">perl-bioperl</requirement>
      <requirement type="package">perl-moose</requirement>
      <requirement type="package">perl-ipc-run</requirement>
      <requirement type="package">perl-getopt-long-descriptive</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
perl -Mlib=$__tool_directory__/lib $__tool_directory__/cpt_psm_0_prep.pl
--galaxy
--outfile_supporting $__new_file_path__
#for $item in $repeat_file:
--file "${item.file}"
#end for

--cpt_psm_object "${cpt_psm_object}"

--cpt_psm_object_files_path "${cpt_psm_object.files_path}"

--cpt_psm_object_format "${cpt_psm_object_format}"

--cpt_psm_object_id "${cpt_psm_object.id}"

]]></command>
  <inputs>
    <repeat name="repeat_file" title="File">
      <param name="file" help="Input file" optional="False" label="file" type="data"/>
    </repeat>
    <param name="cpt_psm_object_format" help="Output PSM Object" optional="False" label="Format of cpt_psm_object" type="select">
      <option value="TXT" selected="True">TXT</option>
      <option value="CONF">CONF</option>
    </param>
  </inputs>
  <outputs>
    <data name="cpt_psm_object" format="TXT">
      <change_format>
        <when input="cpt_psm_object_format" value="TXT" format="txt"/>
        <when input="cpt_psm_object_format" value="CONF" format="txt"/>
      </change_format>
    </data>
  </outputs>
  <help>NAME
====

PSM Prep

DESCRIPTION
===========

This tool takes in 2 or more GenBank files, blasts, and prepares data
structures for use in the companion tool: PSM Plotter. Select as many
(multi)-gbk files as you *might* want to plot. Once this tool is done,
you can select any subset of those to plot then.
</help>
  <tests/>
</tool>